Glad to hear you figured this out, new routing setups can be tricky.

Regarding Emote as a plug-in, making the plug-in active/bypassed will not accomplish much. Emote is simply a controller for the H9000; all of the audio routing must be done using the DAW, and the plug-in will still send the control information when it is bypassed. Whether or not you are processing in mono/stereo is determined by your FX Chain routing, and how you are sending audio to the H9000, the Emote plug-in being mono/stereo will not make a difference.

The key features that are available only when using Emote as a plug-in are listed here: https://cdn.eventideaudio.com/manuals/h9000/2.0/content/emote/plugin.html